-
Notifications
You must be signed in to change notification settings - Fork 3
/
Copy pathcli-call-pedigree-help.txt
187 lines (186 loc) · 12.4 KB
/
cli-call-pedigree-help.txt
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
usage: MCMC haplotype calling via pedigree-annealing. [-h]
[--haplotypes HAPLOTYPES]
[--prior-frequencies PRIOR_FREQUENCIES]
[--filter-input-haplotypes FILTER_INPUT_HAPLOTYPES]
[--bam BAM [BAM ...]]
[--ploidy PLOIDY]
[--sample-parents SAMPLE_PARENTS]
[--gamete-ploidy GAMETE_PLOIDY]
[--gamete-ibd GAMETE_IBD]
[--gamete-error GAMETE_ERROR]
[--sample-pool SAMPLE_POOL]
[--reference REFERENCE]
[--base-error-rate BASE_ERROR_RATE]
[--use-base-phred-scores]
[--mapping-quality MAPPING_QUALITY]
[--keep-duplicate-reads]
[--keep-qcfail-reads]
[--keep-supplementary-reads]
[--read-group-field READ_GROUP_FIELD]
[--report [REPORT ...]]
[--cores CORES]
[--mcmc-chains MCMC_CHAINS]
[--mcmc-steps MCMC_STEPS]
[--mcmc-burn MCMC_BURN]
[--mcmc-seed MCMC_SEED]
[--mcmc-chain-incongruence-threshold MCMC_CHAIN_INCONGRUENCE_THRESHOLD]
options:
-h, --help show this help message and exit
--haplotypes HAPLOTYPES
Tabix indexed VCF file containing haplotype/MNP/SNP
variants to be re-called among input samples.
--prior-frequencies PRIOR_FREQUENCIES
Optionally specify an INFO field within the input VCF
file to designate as prior allele frequencies for the
input haplotypes. This can be any numerical field of
length 'R' and these values will automatically be
normalized.
--filter-input-haplotypes FILTER_INPUT_HAPLOTYPES
Optionally filter input haplotypes using a string of
the form '<field><operator><value>' where <field> is a
numerical INFO field with length 'A' or 'R',
<operator> is one of =|>|<|>=|<=|!=, and <value> is a
numerical value.
--bam BAM [BAM ...] Bam file(s) to use in analysis. This may be (1) a list
of one or more bam filepaths, (2) a plain-text file
containing a single bam filepath on each line, (3) a
plain-text file containing a sample identifier and its
corresponding bam filepath on each line separated by a
tab. If options (1) or (2) are used then all samples
within each bam will be used within the analysis. If
option (3) is used then only the specified sample will
be extracted from each bam file and An error will be
raised if a sample is not found within its specified
bam file.
--ploidy PLOIDY Specify sample ploidy (default = 2).This may be (1) a
single integer used to specify the ploidy of all
samples or (2) a file containing a list of all samples
and their ploidy. If option (2) is used then each line
of the plaintext file must contain a single sample
identifier and the ploidy of that sample separated by
a tab.
--sample-parents SAMPLE_PARENTS
A file containing a list of samples and their parents
used to indicate pedigree structure. Each line should
contain a sample identifier followed by both parent
identifiers separated by tabs. A period '.' is used to
indicate unknown parents.
--gamete-ploidy GAMETE_PLOIDY
Ploidy of the gametes contributing to each sample. By
default it is assumed that the ploidy of each gamete
is equal to half the ploidy of the sample derived from
that gamete. If all gametes have the same ploidy then
a single number can be specified. If gametic ploidy is
variable then these values must be specified with a
file containing a list of samples and the ploidy of
the gametes they were derived from. Each line of this
file should contain a sample identifier followed by
the ploidy of gametes derived from each parent in the
same order as specified using the --sample-parents
argument. For each sample, the ploidy of the two
gametes must sum to the ploidy of that sample.
--gamete-ibd GAMETE_IBD
Excess IBD/homozygosity due to meiotic processes. By
default this variable is 0.0 for all gametes and non-
zero values may only be specified for gametes with a
ploidy of 2. This value must be in the interval [0, 1]
with a value of 0.0 indicating no excess
ibd/homozygosity and a value of 1.0 indicating that
the gamete must be fully homozygous.If a single value
is specified then this will be applied to all gametes.
If this value varies between gametes then it must be
specified with a file containing a list of samples and
the value associated with each gamete those samples
are derived from. Each line should contain a sample
identifier followed by value of each gamete in the
same order as specified using the --sample-parents
argument.
--gamete-error GAMETE_ERROR
An error term associated with each parent-child pair
indicating the probability that that gamete was not
derived from the specified parent. By default this
variable is 0.01 for all parent-child pairs. This
value must be in the interval [0, 1] and should
generally be > 0 and < 1.If a single value is
specified then this will be applied to all parent-
child pairs. If this value varies between gametes then
it must be specified with a file containing a list of
samples and the value associated with each gamete
those samples are derived from. Each line should
contain a sample identifier followed by value of each
gamete in the same order as specified using the
--sample-parents argument.
--sample-pool SAMPLE_POOL
WARNING: this is an experimental feature!!! Pool
samples together into a single genotype. This may be
(1) the name of a single pool for all samples or (2) a
file containing a list of all samples and their
assigned pool. If option (2) is used then each line of
the plaintext file must contain a single sample
identifier and the name of a pool separated by a
tab.Samples may be assigned to multiple pools by using
the same sample name on multiple lines.Each pool will
treated as a single genotype by combining all reads
from its constituent samples. Note that the pool names
should be used in place of the samples names when
assigning other per-sample parameters such as ploidy
or inbreeding coefficients.
--reference REFERENCE
Indexed fasta file containing the reference genome.
--base-error-rate BASE_ERROR_RATE
Expected base error rate of read sequences (default =
0.0024). The default value comes from Pfeiffer et al
2018 and is a general estimate for Illumina short
reads.
--use-base-phred-scores
Flag: use base phred-scores as a source of base error
rate. This will use the phred-encoded per base scores
in addition to the general error rate specified by the
--base-error-rate argument. Using this option can slow
down assembly speed.
--mapping-quality MAPPING_QUALITY
Minimum mapping quality of reads used in assembly
(default = 20).
--keep-duplicate-reads
Flag: Use reads marked as duplicates in the assembly
(these are skipped by default).
--keep-qcfail-reads Flag: Use reads marked as qcfail in the assembly
(these are skipped by default).
--keep-supplementary-reads
Flag: Use reads marked as supplementary in the
assembly (these are skipped by default).
--read-group-field READ_GROUP_FIELD
Read group field to use as sample id (default = "SM").
The chosen field determines tha sample ids required in
other input files e.g. the --sample-list argument.
--report [REPORT ...]
Extra fields to report within the output VCF. The
INFO/FORMAT prefix may be omitted to return both
variations of the named field. Options include:
INFO/AFPRIOR = Prior allele frequencies; INFO/ACP =
Posterior allele counts; INFO/AFP = Posterior mean
allele frequencies; INFO/AOP = Posterior probability
of allele occurring across all samples; INFO/AOPSUM =
Posterior estimate of the number of samples containing
an allele; INFO/SNVDP = Read depth at each SNV
position; FORMAT/ACP: Posterior allele counts;
FORMAT/AFP: Posterior mean allele frequencies;
FORMAT/AOP: Posterior probability of allele occurring;
FORMAT/GP: Genotype posterior probabilities;
FORMAT/GL: Genotype likelihoods; FORMAT/SNVDP: Read
depth at each SNV position
--cores CORES Number of cpu cores to use (default = 1).
--mcmc-chains MCMC_CHAINS
Number of independent MCMC chains per assembly
(default = 2).
--mcmc-steps MCMC_STEPS
Number of steps to simulate in each MCMC chain
(default = 2000).
--mcmc-burn MCMC_BURN
Number of initial steps to discard from each MCMC
chain (default = 1000).
--mcmc-seed MCMC_SEED
Random seed for MCMC (default = 42).
--mcmc-chain-incongruence-threshold MCMC_CHAIN_INCONGRUENCE_THRESHOLD
Posterior probability threshold for identification of
incongruent posterior modes (default = 0.60).